ZBTB38

zinc finger and BTB domain containing 38, the group of Zinc fingers C2H2-type|BTB domain containing

Basic information

Region (hg38): 3:141324213-141449792

Links

ENSG00000177311 ∙ NCBI:253461 ∙ OMIM:612218 ∙ HGNC:26636 ∙ Uniprot:Q8NAP3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZBTB38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB38 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			42	4	2	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	4	4

Variants in ZBTB38

This is a list of pathogenic ClinVar variants found in the ZBTB38 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-141442467-C-G		not specified	Uncertain significance (Jun 07, 2022)
3-141442474-G-A		not specified	Uncertain significance (Dec 03, 2021)
3-141442761-C-T		not specified	Uncertain significance (Mar 04, 2024)
3-141442951-G-A		not specified	Uncertain significance (Oct 26, 2022)
3-141443021-G-C			Benign (Jul 04, 2018)
3-141443029-C-A		not specified	Uncertain significance (Dec 05, 2022)
3-141443212-C-T		not specified	Uncertain significance (May 10, 2022)
3-141443295-G-A		not specified	Uncertain significance (Aug 02, 2023)
3-141443316-C-G		not specified	Uncertain significance (Mar 25, 2024)
3-141443404-C-T		not specified	Uncertain significance (Feb 06, 2023)
3-141443452-C-T		not specified	Uncertain significance (Sep 26, 2023)
3-141443488-C-T		not specified	Uncertain significance (Jun 18, 2021)
3-141443496-C-A		not specified	Uncertain significance (Jun 30, 2022)
3-141443551-G-A		not specified	Uncertain significance (Jul 05, 2022)
3-141443557-A-T		not specified	Uncertain significance (Jun 06, 2023)
3-141443608-G-A		not specified	Uncertain significance (May 03, 2023)
3-141443634-G-A		not specified	Uncertain significance (Jun 30, 2022)
3-141443647-G-T		not specified	Uncertain significance (May 16, 2024)
3-141443709-G-A		not specified	Uncertain significance (Jul 11, 2023)
3-141443760-A-G		not specified	Uncertain significance (Dec 08, 2023)
3-141443785-A-G		not specified	Uncertain significance (Feb 28, 2024)
3-141443974-A-G		not specified	Uncertain significance (Nov 22, 2022)
3-141444106-G-C		not specified	Uncertain significance (Dec 19, 2022)
3-141444133-G-A		not specified	Uncertain significance (Mar 13, 2023)
3-141444157-G-A		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB38	protein_coding	protein_coding	ENST00000514251	1	125580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000509	124756	0	5	124761	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.31	494	661	0.747	0.0000364	7956
Missense in Polyphen		125	264.46	0.47267		3243
Synonymous	1.52	227	258	0.879	0.0000161	2260
Loss of Function	5.02	3	35.1	0.0856	0.00000195	468

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator with bimodal DNA-binding specificity. Binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' but can also bind to E-box elements (5'-CACGTG-3'). Can also bind specifically to a single methyl-CpG pair. Represses transcription in a methyl- CpG-dependent manner (PubMed:16354688). Plays an important role in regulating DNA replication and common fragile sites (CFS) stability in a RBBP6- and MCM10-dependent manner; represses expression of MCM10 which plays an important role in DNA- replication (PubMed:24726359). Acts as a transcriptional activator. May be involved in the differentiation and/or survival of late postmitotic neurons (By similarity). {ECO:0000250|UniProtKB:Q5EXX3, ECO:0000269|PubMed:16354688, ECO:0000269|PubMed:24726359}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.0810
• rvis_EVS: 0.03
• rvis_percentile_EVS: 55.81

Haploinsufficiency Scores

• pHI: 0.476
• hipred: Y
• hipred_score: 0.629
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.806

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Zbtb38

Gene ontology

• Biological process: regulation of DNA replication;regulation of transcription, DNA-templated;cellular response to DNA damage stimulus;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;chromosome;blood microparticle
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;methyl-CpG binding;protein homodimerization activity;metal ion binding